I have a 400 watt servo motor with a driver which needs some pulses to move the motor and control its speed , it can count the encoder pulses, includes electronic gears and many thing else .
is the motion controller card a replacement for the motor driver, or a motion controller card should be used next to the motor driver to create the pulse trains and also read the encoder outputs ?
In general, a motion controller and a driver are two different things:
See here for an overview from National Instruments.